F-box proteins (FBPs) represent one of the largest and fastest evolving
gene/protein families in the plant kingdom. The FBP superfamily can be
divided in several subfamilies characterized by different C-terminal
protein-protein interaction domains that recruit targets for proteasomal
degradation. Hence, a clear picture of their phylogeny and molecular
evolution is of special interest for the general understanding of
evolutionary histories of multi-domain and/or large protein families in
plants. In an effort to further understand the molecular evolution of
F-box family proteins, we asked whether the largest subfamily in Arabidopsis thaliana,
which carries a C-terminal F-box associated domain (FBA proteins)
shares evolutionary patterns and signatures of selection with other
FBPs. To address this question, we applied phylogenetic and molecular
evolution analyses in combination with the evaluation of transcriptional
profiles. Based on the 2219 FBA proteins we de novo identified
in 34 completely sequenced plant genomes, we compared their
evolutionary patterns to a previously analyzed large subfamily carrying
C-terminal kelch repeats. We found that these two large FBP subfamilies
generally tend to evolve by massive waves of duplication, followed by
sequence conservation of the F-box domain and sequence diversification
of the target recruiting domain. We conclude that the earlier in
evolutionary time a major wave of expansion occurred, the more
pronounced these selection signatures are. As a consequence, when
performing cross species comparisons among FBP subfamilies, significant
differences will be observed in the selective signatures of
protein-protein interaction domains. Depending on the species, the
investigated subfamilies comprise up to 45% of the complete superfamily,
indicating that other subfamilies possibly follow similar modes of
evolution.

TIR1/AFBTIR1The COP9 signalosome (CSN) is an eight subunit protein complex conserved in all higher eukaryotes. In Arabidopsis thaliana, the CSN regulates auxin response by removing the ubiquitin-like protein NEDD8/RUB1 from the CUL1 subunit of the SCF ubiquitin-ligase (deneddylation). Previously described null mutations in any CSN subunit result in the pleiotropic cop/det/fus
phenotype and cause seedling lethality, hampering the study of CSN
functions in plant development. In a genetic screen to identify
enhancers of the auxin response defects conferred by the tir1-1 mutation, we identified a viable csn mutant of subunit 3 (CSN3), designated eta7/csn3-3. In addition to enhancing tir1-1 mutant phenotypes, the csn3-3
mutation alone confers several phenotypes indicative of impaired auxin
signaling including auxin resistant root growth and diminished auxin
responsive gene expression. Unexpectedly however, csn3-3 plants are not defective in either the CSN-mediated deneddylation of CUL1 or in SCF-mediated degradation of Aux/IAA proteins. These findings suggest that csn3-3 is an atypical csn
mutant that defines a novel CSN or CSN3-specific function. Consistent
with this possibility, we observe dramatic differences in double mutant
interactions between csn3-3 and other auxin signaling mutants compared to another weak csn mutant, csn1-10. Lastly, unlike other csn mutants, assembly of the CSN holocomplex is unaffected in csn3-3 plants. However, we detected a small CSN3-containing protein complex that is altered in csn3-3
plants. We hypothesize that in addition to its role in the CSN as a
cullin deneddylase, CSN3 functions in a distinct protein complex that is
required for proper auxin signaling.